MolNFT v1 · #116826 · protein

Crystal structure of PLEKHM1 lir-fused human GABARAP_2-117

5DPS · Pleckstrin homology domain-containing family M member 1…: “Crystal structure of PLEKHM1 lir-fused human GABARAP_2-117”. X-ray diffraction, 5 pockets (best druggability 0.51). MolNFT v1 #116826 on GenesisL1: 3D structure, binding…

PDB: 5DPS
Type: protein
Length: 365 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid…
UniProt: Q9Y4G2, O95166
Pockets: 5 · best druggability 0.51

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein	protein	122	32% helix, 21% strand	Q9Y4G2, O95166
B	Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein	protein	122	31% helix, 23% strand	Q9Y4G2, O95166
C	Pleckstrin homology domain-containing family M member 1, gamma-aminobutyric acid receptor-associated protein	protein	121	31% helix, 23% strand	Q9Y4G2, O95166

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	187	0.51	0.77	36	empty
2	118	0.43	0.77	23	empty
3	78	0.39	0.78	24	empty
4	54	0.34	0.78	17	empty
5	60	0.29	0.75	18	empty

Interfaces

2 interfaces between chains.

A–B · 395 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 278 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5DPS · Crystal structure of PLEKHM1 LIR-fused human GABARAP_2-117 · the same entry in another collection · chain A against A, TM-score 1.00
O95166 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated protein… · a predicted model of the same protein · chain C against A, TM-score 0.93
Q9Y4G2 · AlphaFold monomer V2.0 prediction for pleckstrin homology domain- containing family M… · a predicted model of the same protein · chain B against A, TM-score 0.33

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y4G2
Every structure of UniProt O95166
Elsewhere: RCSB PDB 5DPS · PDBe 5DPS · UniProt Q9Y4G2 · UniProt O95166

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